Wrapper to clean UID temperature CSV: read, flag outliers, downsample, and plot

The cleaning workflow assumes that each rfid belongs to a single matrix_name within a session. If the same rfid is detected on more than one matrix, the function prints a summary table with session_name, rfid, matrix_name, n, %, min_dt, and max_dt.

Usage

clean_raw_uid(
  filepath,
  n = 1,
  precision = "minute",
  outlier_threshold_celsius = 1,
  output_dir = "temperature/data",
  plot = TRUE,
  flicker_correction = TRUE,
  flicker_dominant_two_thr = 0.65,
  flicker_alt_rate_thr = 0.4,
  flicker_contiguous_thr = 0.65
)

Arguments

filepath: Path to a raw UID CSV.
n: Downsampling interval size (default = 1) applied to both temperature and activity data.
precision: Time unit for downsampling (default = "minute").
outlier_threshold_celsius: Temperature difference threshold to flag outliers.
output_dir: Directory to save diagnostic plots.
plot: boolean to indicate whether to plot the process of outlier removal and downsampling
flicker_correction: Whether to apply activity flicker correction before quantification.
flicker_dominant_two_thr: Threshold for dominant two-zone occupancy fraction.
flicker_alt_rate_thr: Threshold for ABAB alternation rate within minute bins.
flicker_contiguous_thr: Threshold for fraction of contiguous transitions within minute bins.

Value

A list with cleaned, downsampled temperature and activity data frames.

Details

Low-percentage duplicate detections can happen when matrices are placed too close to each other or when a cage is briefly placed on the wrong platform. In those cases, the function asks for explicit confirmation before removing rows from the matrix with the lower percentage of detections. If duplicate measurements on the secondary matrix exceed 10% of detections for that session_name/rfid pair, the function aborts and requires manual review.